get_sub_clusters: Detect sub clusters

In Kumquatum/GWENA: Pipeline for augmented co-expression analysis

Detect sub clusters

Description

Use a partitioning around medoid (PAM, or k-medoid) clustering method to detect clusters into a provided module using the strength matrix of the network

Usage

get_sub_clusters(network, seq_k = seq_len(15), fit_plot = TRUE, ...)

Arguments

network	matrix or data.frame, strength of gene co-expression (edge values).
seq_k	vector, sequence of k number of cluster to test
fit_plot	boolean, does the plot with silhouette coefficient depending on the k tested should be plotted.
...	any other parameter compatible with the pam function.

Value

data.frame, a two cols table with the gene id in the first one, and the cluster number assignation in the second one.

Examples

df <- kuehne_expr[1:24, 1:350]
net <- build_net(df, n_threads = 1)
mods <- detect_modules(df, net$network)
net_mod_1 <- net$network[mods$modules$`1`, mods$modules$`1`]
get_sub_clusters(net_mod_1)

Kumquatum/GWENA documentation built on July 7, 2023, 3:41 p.m.